Purpose The current study aimed to assess the changes in physical and perceptual markers of health, fitness, and well-being over the first semester of university study in a New Zealand context. Methods In a pre-post longitudinal design, 90 first-year university students (39 females, 51 males, mean ± SD age: 18 ± 2 years) studying in the field of health, sport and human performance underwent tests of body mass, height, body mass index (BMI), blood pressure, predicted VO 2max , flexibility, countermovement jump height, handgrip strength, isometric mid-thigh pull strength, and well-being pre and post the first semester of university study (12 weeks). Results When evaluating the entire group, there was a significant increase in body mass (0.66 kg, P = 0.004) and BMI (0.2 kg/m 2 , P = 0.005) and decrease in the "engagement" construct of the well-being questionnaire (− 0.2, P = 0.03) over the first semester of university. In total, 73% of students living on-campus reported a decline in sleep and nutrition habits since starting university, in comparison to ~ 35%-40% of students living off-campus (P ≤ 0.03). Conclusion Similar to results seen in other countries, and despite the field of study, the first semester of university in New Zealand is likely to be associated with increases in body mass and BMI; however, changes in physical fitness and overall well-being measures were less obvious in the current study.